validate-scripts.yml

name: Validate Scripts

on:
  push:
    branches: ['**']
  pull_request:
    branches: [main]

jobs:
  syntax-check:
    name: Bash Syntax Check
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Check bash syntax with bash -n
        run: |
          echo "Checking syntax of all .sh files..."
          failed=0
          count=0
          while IFS= read -r file; do
            if ! bash -n "$file" 2>/tmp/syntax_err; then
              echo "FAIL: $file"
              cat /tmp/syntax_err
              failed=$((failed + 1))
            fi
            count=$((count + 1))
          done < <(find . -name '*.sh' -not -path './.git/*' | sort)
          echo ""
          echo "Checked $count files, $failed failed"
          [ "$failed" -eq 0 ]

  shellcheck:
    name: ShellCheck (advisory)
    runs-on: ubuntu-latest
    continue-on-error: true
    steps:
      - uses: actions/checkout@v4

      - name: Install shellcheck
        run: sudo apt-get update && sudo apt-get install -y shellcheck

      - name: Run shellcheck --severity=error
        run: |
          echo "Running shellcheck (error-level only)..."
          failed=0
          count=0
          while IFS= read -r file; do
            if ! shellcheck --severity=error "$file" 2>/dev/null; then
              failed=$((failed + 1))
            fi
            count=$((count + 1))
          done < <(find . -name '*.sh' -not -path './.git/*' | sort)
          echo ""
          echo "Checked $count files, $failed had errors"
          [ "$failed" -eq 0 ]

  unit-tests:
    name: Unit Tests
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Run unit test suites
        run: |
          failed=0
          for suite in tests/test_environment_unit.sh tests/test_pipeline_control_unit.sh tests/test_import_unit.sh; do
            echo ""
            echo "========================================"
            echo "Running: $suite"
            echo "========================================"
            if bash "$suite"; then
              echo "PASS: $suite"
            else
              echo "FAIL: $suite (exit code: $?)"
              failed=$((failed + 1))
            fi
          done
          echo ""
          echo "========================================"
          if [ "$failed" -gt 0 ]; then
            echo "$failed test suite(s) failed"
            exit 1
          else
            echo "All test suites passed"
          fi

  pipeline-smoke-test:
    name: Pipeline Smoke Test
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Verify pipeline.sh --help works
        run: |
          # Provide a dummy FSL config so the early `source $FSLDIR/etc/fslconf/fsl.sh`
          # in pipeline.sh succeeds under `set -e` (no real FSL install in CI).
          export FSLDIR=/tmp/fake_fsl
          mkdir -p "$FSLDIR/etc/fslconf"
          printf '# dummy FSL config for CI smoke test\n' > "$FSLDIR/etc/fslconf/fsl.sh"

          output=$(bash src/pipeline.sh --help 2>&1)
          echo "$output"
          echo ""
          echo "--- Validating help output ---"
          echo "$output" | grep -q "Usage:" || { echo "FAIL: missing Usage line"; exit 1; }
          echo "$output" | grep -q "Pipeline Stages:" || { echo "FAIL: missing Pipeline Stages"; exit 1; }
          echo "PASS: --help output looks correct"

      - name: Verify pipeline loads all modules and fails gracefully on missing tools
        run: |
          # Set required vars to dummy values so module sourcing doesn't crash
          # on unbound variables. The pipeline should still fail at the
          # dependency check stage — that's exactly what we want to verify.
          export FSLDIR=/tmp/fake_fsl
          export ANTS_PATH=/tmp/fake_ants

          # Provide a dummy FSL config so the early `source $FSLDIR/etc/fslconf/fsl.sh`
          # in pipeline.sh succeeds under `set -e` (no real FSL install in CI).
          mkdir -p "$FSLDIR/etc/fslconf"
          printf '# dummy FSL config for CI smoke test\n' > "$FSLDIR/etc/fslconf/fsl.sh"

          echo "Running pipeline.sh with no input data..."
          output=$(bash src/pipeline.sh 2>&1 || true)
          echo "$output"
          echo ""
          echo "--- Validating module loading ---"

          check() {
            if echo "$output" | grep -q "$1"; then
              echo "PASS: found '$1'"
            else
              echo "FAIL: missing '$1'"
              return 1
            fi
          }

          failed=0

          # Confirm key modules loaded successfully
          check "Environment module loaded"          || failed=$((failed + 1))
          check "Import module loaded"               || failed=$((failed + 1))
          check "Registration module loaded"         || failed=$((failed + 1))
          check "Segmentation module loaded"         || failed=$((failed + 1))
          check "Analysis module loaded"             || failed=$((failed + 1))
          check "Visualization module loaded"        || failed=$((failed + 1))

          # Confirm pipeline got past module loading to actual execution
          check "Arguments parsed:"                  || failed=$((failed + 1))
          check "Comprehensive Pipeline Dependency Check" || failed=$((failed + 1))

          # Confirm the dependency check section ran (outcome varies by environment)
          check "Dependency Check Summary"           || failed=$((failed + 1))

          echo ""
          if [ "$failed" -gt 0 ]; then
            echo "$failed checks failed — pipeline may not be loading correctly"
            exit 1
          else
            echo "All checks passed — pipeline loads and fails gracefully"
          fi